scholarly journals A Taxonomic Investigation into the Red Alga Plocamium within New Zealand

2021 ◽  
Author(s):  
◽  
Madeline Wynn Cooper
Keyword(s):  
New Zealand ◽  
Species Delimitation ◽  
Phylogenetic Analyses ◽  
Evolutionary Relationship ◽  
Red Alga ◽  
Morphometric Analyses ◽  
True Diversity ◽  
Candidate Species ◽  
Bayesian Implementation ◽  
Genetic Species

<p>The red alga Plocamium is a cosmopolitan genus, known for its distinct branching pattern and rich chemical composition. Recent studies indicate morphological-based species delimitation approaches have failed to accurately discern diversity, distributions, and evolutionary relationship between species worldwide. Currently there are seven recognized species within New Zealand based on traditional morphological approaches and no molecular based work focused on discerning true diversity of New Zealand species in this genus. This thesis is the first to use molecular-assisted alpha taxonomy to investigate Plocamium within New Zealand. Phylogenetic analyses (Maximum Likelihood and Bayesian Inference) based on COI, rbcL, LSU and combined LSU/COI markers, three molecular species delimitation methods (Automatic Barcode Gap Discovery, General Mixed Yule Coalescent, and Bayesian implementation of the Poisson Tree Processes), and morphometric analyses of various characters (width of main axis (WMA), width of lowest basal ramuli (WLBR), length of lowest basal ramuli (LLBR), number of alternating series of ramuli (NASR), average number of ramuli per alternating series (ANRAS), curvature of basal ramuli (CBR) and serrations present or absent from basal ramuli (SERBR) were used to address this topic. The species delimitation methods revealed at least eleven (A-K) putative genetic species (with some incongruences) within the New Zealand specimens included in the study. Morphometric analyses indicated morphology reflects genetic diversity when multiple measures of multiple characters are used, however this is not the case when considering single characters. Phylogenetic analyses revealed possible monophyly of New Zealand candidate species C-K, and possible relationships to Australian, Chilean, and Taiwanese species. However these backbone relationships were poorly supported. The results of this study indicate that Plocamium diversity within New Zealand has been underestimated and provide the first steps in discovering the true species diversity of Plocamium within New Zealand.</p>

scholarly journals A Taxonomic Investigation into the Red Alga Plocamium within New Zealand

2021 ◽  
Author(s):  
◽  
Madeline Wynn Cooper
Keyword(s):  
New Zealand ◽  
Species Delimitation ◽  
Phylogenetic Analyses ◽  
Evolutionary Relationship ◽  
Red Alga ◽  
Morphometric Analyses ◽  
True Diversity ◽  
Candidate Species ◽  
Bayesian Implementation ◽  
Genetic Species

<p>The red alga Plocamium is a cosmopolitan genus, known for its distinct branching pattern and rich chemical composition. Recent studies indicate morphological-based species delimitation approaches have failed to accurately discern diversity, distributions, and evolutionary relationship between species worldwide. Currently there are seven recognized species within New Zealand based on traditional morphological approaches and no molecular based work focused on discerning true diversity of New Zealand species in this genus. This thesis is the first to use molecular-assisted alpha taxonomy to investigate Plocamium within New Zealand. Phylogenetic analyses (Maximum Likelihood and Bayesian Inference) based on COI, rbcL, LSU and combined LSU/COI markers, three molecular species delimitation methods (Automatic Barcode Gap Discovery, General Mixed Yule Coalescent, and Bayesian implementation of the Poisson Tree Processes), and morphometric analyses of various characters (width of main axis (WMA), width of lowest basal ramuli (WLBR), length of lowest basal ramuli (LLBR), number of alternating series of ramuli (NASR), average number of ramuli per alternating series (ANRAS), curvature of basal ramuli (CBR) and serrations present or absent from basal ramuli (SERBR) were used to address this topic. The species delimitation methods revealed at least eleven (A-K) putative genetic species (with some incongruences) within the New Zealand specimens included in the study. Morphometric analyses indicated morphology reflects genetic diversity when multiple measures of multiple characters are used, however this is not the case when considering single characters. Phylogenetic analyses revealed possible monophyly of New Zealand candidate species C-K, and possible relationships to Australian, Chilean, and Taiwanese species. However these backbone relationships were poorly supported. The results of this study indicate that Plocamium diversity within New Zealand has been underestimated and provide the first steps in discovering the true species diversity of Plocamium within New Zealand.</p>

scholarly journals Hidden biodiversity revealed by integrated morphology and genetic species delimitation of spring dwelling water mite species (Acari, Parasitengona: Hydrachnidia)

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Lucas Blattner ◽  
Reinhard Gerecke ◽  
Stefanie von Fumetti
Keyword(s):  
Species Identification ◽  
Molecular Species ◽  
Species Delimitation ◽  
Mite Species ◽  
Water Mites ◽  
Water Mite ◽  
Barcoding Gap ◽  
Molecular Species Identification ◽  
True Diversity ◽  
Genetic Species

Abstract Background Water mites are among the most diverse organisms inhabiting freshwater habitats and are considered as substantial part of the species communities in springs. As parasites, Hydrachnidia influence other invertebrates and play an important role in aquatic ecosystems. In Europe, 137 species are known to appear solely in or near springheads. New species are described frequently, especially with the help of molecular species identification and delimitation methods. The aim of this study was to verify the mainly morphology-based taxonomic knowledge of spring-inhabiting water mites of central Europe and to build a genetic species identification library. Methods We sampled 65 crenobiontic species across the central Alps and tested the suitability of mitochondrial (cox1) and nuclear (28S) markers for species delimitation and identification purposes. To investigate both markers, distance- and phylogeny-based approaches were applied. The presence of a barcoding gap was tested by using the automated barcoding gap discovery tool and intra- and interspecific genetic distances were investigated. Furthermore, we analyzed phylogenetic relationships between different taxonomic levels. Results A high degree of hidden diversity was observed. Seven taxa, morphologically identified as Bandakia concreta Thor, 1913, Hygrobates norvegicus (Thor, 1897), Ljania bipapillata Thor, 1898, Partnunia steinmanni Walter, 1906, Wandesia racovitzai Gledhill, 1970, Wandesia thori Schechtel, 1912 and Zschokkea oblonga Koenike, 1892, showed high intraspecific cox1 distances and each consisted of more than one phylogenetic clade. A clear intraspecific threshold between 5.6–6.0% K2P distance is suitable for species identification purposes. The monophyly of Hydrachnidia and the main superfamilies is evident with different species clearly separated into distinct clades. cox1 separates water mite species but is unsuitable for resolving higher taxonomic levels. Conclusions Water mite species richness in springs is higher than has been suggested based on morphological species identification alone and further research is needed to evaluate the true diversity. The standard molecular species identification marker cox1 can be used to identify species but should be complemented by a nuclear marker, e.g. 28S, to resolve taxonomic relationships. Our results contribute to the taxonomical knowledge on spring inhabiting Hydrachnida, which is indispensable for the development and implementation of modern environment assessment methods, e.g. metabarcoding, in spring ecology.

Exploring the diversity of Asian Cryptocercus (Blattodea : Cryptocercidae): species delimitation based on chromosome numbers, morphology and molecular analysis

2018 ◽  
Vol 32 (1) ◽  
pp. 69 ◽  
Author(s):  
Qikun Bai ◽  
Lili Wang ◽  
Zongqing Wang ◽  
Nathan Lo ◽  
Yanli Che
Keyword(s):  
Chromosome Number ◽  
Species Delimitation ◽  
Phylogenetic Analyses ◽  
Western China ◽  
Tibet Plateau ◽  
28S Rrna ◽  
Candidate Species ◽  
The Rich ◽  
Coi Sequences ◽  
Qinghai Tibet Plateau

Woodroaches from the genus Cryptocercus Scudder, 1862 are known to display low levels of morphological divergence, yet significant genetic divergence and variability in chromosome number. Compared with Cryptocercus taxa from North America, the diversity of the genus in Asia has received relatively little attention. We performed morphological and karyotypic examinations of multiple taxa from several previously unsampled mountainous areas of central and south-western China, and identified nine candidate species primarily on the basis of chromosome number. We then investigated diversity across all Asian Cryptocercus, through phylogenetic analyses of 135 COI sequences and 74 28S rRNA sequences from individuals of 28 localities, including species delimitation analysis in General Mixed Yule Coalescent (GMYC) and Automatic Barcode Gap Discovery (ABGD). Phylogenetic results indicated that individuals from the same locality constituted well supported clades. The congruence of GMYC and ABGD results were in almost perfect accord, with 28 candidate species described on the basis of karyotypes (including the nine identified in this study). We provide evidence that each valley population in the Hengduan Mountains contains a separate evolving lineage. We conclude that the principal cause of the rich Cryptocercus diversity in China has been the uplift of the Qinghai-Tibet Plateau.

scholarly journals Linking morphological and molecular sources to disentangle the case of Xylodon australis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Javier Fernández-López ◽  
M. Teresa Telleria ◽  
Margarita Dueñas ◽  
Mara Laguna-Castro ◽  
Klaus Schliep ◽  
...  
Keyword(s):  
New Zealand ◽  
Phylogenetic Analyses ◽  
Single Species ◽  
R Package ◽  
Molecular Data ◽  
Historical Collections ◽  
Close Relationship ◽  
Kinship Relations ◽  
History Of ◽  
Different Sources

AbstractThe use of different sources of evidence has been recommended in order to conduct species delimitation analyses to solve taxonomic issues. In this study, we use a maximum likelihood framework to combine morphological and molecular traits to study the case of Xylodon australis (Hymenochaetales, Basidiomycota) using the locate.yeti function from the phytools R package. Xylodon australis has been considered a single species distributed across Australia, New Zealand and Patagonia. Multi-locus phylogenetic analyses were conducted to unmask the actual diversity under X. australis as well as the kinship relations respect their relatives. To assess the taxonomic position of each clade, locate.yeti function was used to locate in a molecular phylogeny the X. australis type material for which no molecular data was available using morphological continuous traits. Two different species were distinguished under the X. australis name, one from Australia–New Zealand and other from Patagonia. In addition, a close relationship with Xylodon lenis, a species from the South East of Asia, was confirmed for the Patagonian clade. We discuss the implications of our results for the biogeographical history of this genus and we evaluate the potential of this method to be used with historical collections for which molecular data is not available.

scholarly journals Species delimitation and phylogeny of a New Zealand plant species radiation

2009 ◽  
Vol 9 (1) ◽  
pp. 111 ◽  
Author(s):  
Heidi M Meudt ◽  
Peter J Lockhart ◽  
David Bryant
Keyword(s):  
New Zealand ◽  
Plant Species ◽  
Species Delimitation ◽  
Species Radiation

Genetic and morphological diversity of the cosmopolitan chaetognath Pseudosagitta maxima (Conant, 1896) in the Atlantic Ocean and its relationship with the congeneric species

2017 ◽  
Vol 74 (7) ◽  
pp. 1875-1884 ◽  
Author(s):  
Dmitry N. Kulagin ◽  
Tatiana V. Neretina
Keyword(s):  
Atlantic Ocean ◽  
Large Scale ◽  
Phylogenetic Analyses ◽  
Morphological Diversity ◽  
Maturity Stage ◽  
Congeneric Species ◽  
Morphological Examination ◽  
Posterior Teeth ◽  
Biogeographic Patterns ◽  
True Diversity

Abstract Until recently many oceanic zooplankton species have been considered as cosmopolitan organisms. At present it became evident that some of them comprise many distinct molecular operational taxonomic units (MOTUs) that often are regarded as cryptic species. As they can significantly change our perceptions of large-scale biogeographic patterns, it is important to characterize the true diversity within common and ecologically important groups. We have analysed the molecular and morphological diversity of the cosmopolitan mesopelagic chaetognath Pseudosagitta maxima throughout the Atlantic Ocean from 60° S to 85° N and its position within the genus Pseudosagitta. Three distinct mitochondrial clades within P. maxima were revealed with phylogenetic analyses (Maximum Likelihood, Bayesian Inference) and were geographically separated. The subsequent analyses of nuclear markers (H3, ITS1) have shown that P. maxima most likely comprises two distinct MOTUs, tropical and bipolar, that also have some morphological differences. The latter MOTU consists of two genetically slightly divergent populations: southern and northern. The morphological examination allowed the determination of a character (type of hook coloration) that accurately distinguishes juveniles of the P. maxima complex from the other congeneric species. Molecular data have shown that evolutionary P. lyra and P. gazellae are more closely related to each other than to P. maxima. Number of hooks, number of anterior and posterior teeth and the arrangement of ova in the ovary were proposed to be the most useful morphological characters to distinguish between tropical and bipolar MOTUs within the P. maxima complex. The first three characters should be determined for each maturity stage separately.

Molecular systematics of Thouarella (Octocorallia:Primnoidae) with the description of three new species from the Southern Ocean based on combined molecular and morphological evidence

2021 ◽  
Author(s):  
Mónica Núñez-Flores ◽  
Daniel Gomez-Uchida ◽  
Pablo J. López-González
Keyword(s):  
New Species ◽  
Southern Ocean ◽  
Species Delimitation ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Weddell Sea ◽  
Morphological Evidence ◽  
Three New Species ◽  
Taxonomic Framework ◽  
The Antarctic

Thouarella Gray, 1870, is one of the most speciose genera among gorgonians of the family Primnoidae (Cnidaria:Octocorallia:Anthozoa), being remarkably diverse in the Antarctic and sub-Antarctic seafloor. However, their diversity in the Southern Ocean is likely underestimated. Phylogenetic analyses of mitochondrial and nuclear DNA markers were integrated with species delimitation approaches as well as morphological colonial and polyps features and skeletal SEM examinations to describe and illustrate three new species within Thouarella, from the Weddell Sea, Southern Ocean: T. amundseni sp. nov., T. dolichoespinosa sp. nov. and T. pseudoislai sp. nov. Our species delimitation results suggest, for the first time, the potential presence of Antarctic and sub-Antarctic cryptic species of primnoids, based on the likely presence of sibling species within T. undulata and T. crenelata. With the three new species here described, the global diversity of Thouarella has increased to 41 species, 15 of which are endemic to the Antarctic and sub-Antarctic waters. Consequently, our results provide new steps for uncovering the shelf benthonic macrofauna’s hidden diversity in the Southern Ocean. Finally, we recommend using an integrative taxonomic framework in this group of organisms and species delimitation approaches because the distinctions between some Thouarella species based only on a superficial examination of their macro- and micromorphological features is, in many cases, limited.

Multi-gene phylogenetic analyses of New Zealand coralline algae: Corallinapetra Novaezelandiae gen. et sp. nov. and recognition of the Hapalidiales ord. nov.

2015 ◽  
Vol 51 (3) ◽  
pp. 454-468 ◽  
Author(s):  
Wendy A. Nelson ◽  
Judith E. Sutherland ◽  
Tracy J. Farr ◽  
Darren R. Hart ◽  
Kate F. Neill ◽  
...  
Keyword(s):  
New Zealand ◽  
Phylogenetic Analyses ◽  
Coralline Algae

scholarly journals An emergent clade of SARS-CoV-2 linked to returned travellers from Iran

2020 ◽  
Author(s):  
John-Sebastian Eden ◽  
Rebecca Rockett ◽  
Ian Carter ◽  
Hossinur Rahman ◽  
Joep de Ligt ◽  
...  
Keyword(s):  
New Zealand ◽  
Infectious Diseases ◽  
Genome Sequencing ◽  
Phylogenetic Analyses ◽  
Emerging Infectious Diseases ◽  
Whole Genome Sequencing Data ◽  
Viral Diversity ◽  
Whole Genome ◽  
Sequencing Data ◽  
Public Data

AbstractThe SARS-CoV-2 epidemic has rapidly spread outside China with major outbreaks occurring in Italy, South Korea and Iran. Phylogenetic analyses of whole genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases.

scholarly journals Uncovering hidden specific diversity of Andean glassfrogs of theCentrolene buckleyispecies complex (Anura: Centrolenidae)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5856 ◽  
Author(s):  
Luis Amador ◽  
Andrés Parada ◽  
Guillermo D’Elía ◽  
Juan M. Guayasamin
Keyword(s):  
Species Delimitation ◽  
Species Complex ◽  
Behavioral Data ◽  
Nuclear Markers ◽  
Evolutionary Significant Units ◽  
Candidate Species

The glassfrogCentrolene buckleyihas been recognized as a species complex. Herein, using coalescence-based species delimitation methods, we evaluate the specific diversity within this taxon. Four coalescence approaches (generalized mixed Yule coalescents, Bayesian general mixed Yule-coalescent, Poisson tree processes, and Bayesian Poisson tree processes) were consistent with the delimitation results, identifying four lineages within what is currently recognized asC. buckleyi. We propose three new candidate species that should be tested with nuclear markers, morphological, and behavioral data. In the meantime, for conservation purposes, candidate species should be considered evolutionary significant units, in light of observed population crashes in theC. buckleyispecies complex. Finally, our results support the validity ofC. venezuelense, formerly considered as a subspecies ofC. buckleyi.

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